BACKGROUND: Human immunodeficiency virus pre-exposure prophylaxis (PrEP) clinical guidelines recommend men who have sex with men (MSM) PrEP users be screened biannually for syphilis and gonorrhea/chlamydia at all anatomic sites. We sought to determine the proportion screened and positive by STI and anatomic site at PrEP initiation and PrEP-care visits and patient-level characteristics associated with screening among MSM PrEP users in Baltimore City, Maryland. METHODS: Medical records among MSM initiating PrEP between 30 September 2015 and 31 March 2018 were abstracted. STI screening (syphilis and gonorrhea/chlamydia at all anatomic sites) and positivity at PrEP visits ≤12 months following initiation were calculated. Poisson regression with cluster robust SEs was used to assess associations with STI screening. RESULTS: Among 290 MSM initiating PrEP, 43.1% (n = 125) were screened per guidelines at PrEP initiation; 79.3% (230), 69.3% (201), 55.9% (162), and 69.3% (201) were screened for syphilis, urogenital, rectal, and oropharyngeal gonorrhea/chlamydia, respectively. Positivity among those screened was syphilis, 7.8% (n = 18/230); gonorrhea, 5.0% urogenital (10/201), 11.1% rectal (18/162), and 7.5% oropharyngeal (15/201); chlamydia, 5.0% urogenital (10/201), 11.7% rectal (19/162), and 1.5% oropharyngeal (3/201). Reported anal and oral sex (vs neither) was independently associated with STI screening (aPR, 2.11; 1.05-4.27) at PrEP initiation. At biannual PrEP-care visits, STI screening was lower and syphilis and rectal gonorrhea/chlamydia positivity was higher. CONCLUSIONS: Observed STI screening levels and disease burden suggest the effectiveness of STI screening in PrEP care for STI prevention may be limited. Our results suggest providers may be offering screening based on sexual practices; clarification of STI screening guidelines for PrEP users is needed.